Well, no. You can replace the main civ file with this scenario file. In the game registry the main file looks exactly like the editor, and it bears the name 'Conquests.biq'. So if you rename your scenario to 'Conquests.biq' and put it in the game registry like that (back up the existing conquests.biq), then this will be the file used when choosing 'New Game' at set up.
But then if you decide you don't want to play this scenario as your default game, your only option is to make the reverse swap. Although, if a few names extra for Germany is the only difference you made, I don't see how this would affect you when you were not playing as them, so why not use this file all the time?
